CDP-DG(24:0/28:0) (YMDB12636)

Identification
YMDB IDYMDB12636
NameCDP-DG(24:0/28:0)
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionCDP-DG(24:0/28:0) belongs to the family of CDP-diacylglycerols. It is a glycerophospholipid containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. CDP-DG(24:0/28:0), in particular, consists of two tetracosanoyl chain at positions C-1 and C2. In E. coli glycerophospholipid metabolism, The biosynthesis of CDP-diacylglycerol (CDP-DG) involves condensation of phosphatidic acid (PA) and cytidine triphosphate, with elimination of pyrophosphate, catalysed by the enzyme CDP-diacylglycerol synthase. The resulting CDP-diacylglycerol can be utilized immediately for the synthesis of phosphatidylglycerol (PG), and thence cardiolipin (CL), and of phosphatidylinositol (PI). CDP-DG(24:0/28:0) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
SynonymsNot Available
CAS numberNot Available
WeightAverage: 1234.626
Monoisotopic: 1233.827294204
InChI KeyIZTIVHVEBPQJNK-SWWWUWFHSA-N
InChIInChI=1S/C64H121N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-26-27-28-30-32-34-36-38-40-42-44-46-48-50-60(69)80-56(53-77-59(68)49-47-45-43-41-39-37-35-33-31-29-24-22-20-18-16-14-12-10-8-6-4-2)54-78-83(73,74)82-84(75,76)79-55-57-61(70)62(71)63(81-57)67-52-51-58(65)66-64(67)72/h51-52,56-57,61-63,70-71H,3-50,53-55H2,1-2H3,(H,73,74)(H,75,76)(H2,65,66,72)/t56-,57-,61+,62?,63-/m1/s1
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-(octacosanoyloxy)-3-(tetracosanoyloxy)propoxy]phosphoryl}oxy)phosphinic acid
Traditional IUPAC Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-(octacosanoyloxy)-3-(tetracosanoyloxy)propoxy)phosphoryl]oxy)phosphinic acid
Chemical FormulaC64H121N3O15P2
SMILES[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCCC
Chemical Taxonomy
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00021 g/LALOGPS
logP8.85ALOGPS
logP18.45ChemAxon
logS-6.8ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count62ChemAxon
Refractivity332.23 m³·mol⁻¹ChemAxon
Polarizability147.72 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Mitochondrion membrane
Organoleptic PropertiesNot Available
SMPDB Pathways
Cardiolipin Biosynthesis CL(10:0/10:0/24:0/28:0)PW003711 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
PG(10:0/10:0) + CDP-DG(24:0/28:0) → Cytidine monophosphate + hydron + CL(16:0/16:0/16:0/16:0)
PG(10:0/10:0) + CDP-DG(24:0/28:0) → Cytidine monophosphate + hydron + CL(10:0/10:0/24:0/28:0)
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0911100010-038e1498f027d35553feJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1901000001-c5b39a3c9a1bb6903ac4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-4902200000-72af3e4e4a55194da549JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0aos-0927300020-2aff4c19ecbfef733fd8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-02t9-5519200001-c8f6ec61f2565d00e729JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvi-5902000000-8727da971c7dd836bca1JSpectraViewer
References
References:
  • Rattray JB, Schibeci A, Kidby DK. (1975). "Lipids of yeasts." Bacteriol Rev. 1975 Sep;39(3):197-231.240350
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Cardiolipin synthase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
Gene Name:
CRD1
Uniprot ID:
Q07560
Molecular weight:
32019.30078
Reactions
2 Phosphatidylglycerol → diphosphatidylglycerol + glycerol.